Variant report

Variant	rs1016284
Chromosome Location	chr3:118706164-118706165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11709001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709968	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715148	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053925	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1435653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738897	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1836689	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1836691	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879553	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2160050	0.94[ASN][1000 genomes]
rs4405907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687834	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687836	0.82[TSI][hapmap]
rs4687960	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55742142	0.96[ASN][1000 genomes]
rs56232409	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56234333	0.96[ASN][1000 genomes]
rs60755482	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1016284	STXBP6	trans	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118700200-118706200	Enhancers	Brain Hippocampus Middle	brain
2	chr3:118700400-118707800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr3:118701000-118706200	Weak transcription	Psoas Muscle	Psoas
4	chr3:118701600-118709800	Enhancers	Brain Anterior Caudate	brain
5	chr3:118702200-118710600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:118703000-118707800	Enhancers	Fetal Heart	heart
7	chr3:118703200-118707400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:118703600-118707800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:118703600-118708200	Enhancers	Ovary	ovary
10	chr3:118703600-118710000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:118703800-118706200	Weak transcription	Left Ventricle	heart
12	chr3:118704200-118706600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:118704200-118710000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:118704400-118706600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:118704400-118707200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:118704400-118707600	Enhancers	Stomach Smooth Muscle	stomach
17	chr3:118704400-118710200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:118704600-118707600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:118704600-118707800	Enhancers	Brain Germinal Matrix	brain
20	chr3:118704800-118706800	Enhancers	Colon Smooth Muscle	Colon
21	chr3:118704800-118707000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:118704800-118707200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:118705000-118706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:118705200-118706200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:118705200-118706200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:118705200-118706200	Weak transcription	Pancreas	Pancrea
27	chr3:118705200-118706200	Weak transcription	Right Atrium	heart
28	chr3:118705200-118707400	Enhancers	Fetal Brain Female	brain
29	chr3:118705600-118706200	Enhancers	K562	blood
30	chr3:118705600-118707600	Enhancers	Duodenum Mucosa	Duodenum
31	chr3:118705800-118706200	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr3:118705800-118706600	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:118705800-118707400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:118705800-118707600	Enhancers	Fetal Lung	lung
35	chr3:118705800-118709000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:118706000-118706400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr3:118706000-118706400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr3:118706000-118706400	Flanking Active TSS	Fetal Brain Male	brain
39	chr3:118706000-118706400	Enhancers	Fetal Stomach	stomach
40	chr3:118706000-118706600	Enhancers	Aorta	Aorta
41	chr3:118706000-118707200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:118706000-118707600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:118706000-118707800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:118706000-118708200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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